The dark signal degradation of the CMOS image sensor (CIS) was induced by neutron radiation, and it was modeled by Geant4, which is a three-dimensional Monte Carlo code. The simplified model of the CIS array was established according to the actual pixel geometry, material, and doping concentration. Nuclear elastic interaction and capture interaction were included in the physical processes, and the displacement damage dose in the space charge region of the pixel was calculated. The mean dark signal and dark signal distribution were modeled using Geant4, and the physical mechanisms were analyzed. The modeling results were in good agreement with the experimental and theoretical results.